Scientists at ADA Forsyth Institute (AFI) have identified a critical factor that may contribute to the spread of hospital-acquired infections (HAIs), shedding light on why these infections are so difficult to combat. Their study reveals that the dangerous multidrug resistant (MDR) pathogen, Klebsiella, thrives under nutrient-deprived polymicrobial community conditions found in hospital environments.
According to the World Health Organization, HAIs pose significant risks to patients, often resulting in prolonged hospital stays, severe health complications, and a 10% mortality rate. One of the well-known challenging aspects of treating HAIs is the pathogens’ MDR. In a recent study published in Microbiome, AFI scientists discovered that Klebsiella colonising a healthy person not only have natural MDR capability, but also dominate the bacterial community when starved of nutrients.
“Our research demonstrated that Klebsiella can outcompete other microorganisms in its community when deprived of nutrients,” said Batbileg Bor, PhD, associate professor at AFI and principal investigator of the study. “We analysed samples of saliva and nasal fluids to observe Klebsiella‘s response to starvation conditions. Remarkably, in such conditions, Klebsiella rapidly proliferates, dominating the entire microbial community as all other bacteria die off.”
Starvation environments
Klebsiella is one of the top three pathogens responsible for HAIs, including pneumonia and irritable bowel disease. As colonising opportunistic pathogens, they naturally inhabit the oral and nasal cavities of healthy individuals but can become pathogenic under certain conditions. “Hospital environments provide ideal conditions for Klebsiella to spread,” explained Dr Bor. “Nasal or saliva droplets on hospital surfaces, sink drains, and the mouths and throats of patients on ventilators, are all starvation environments.”
Dr Bor further elaborated, “When a patient is placed on a ventilator, they stop receiving food by mouth, causing the bacteria in their mouth to be deprived of nutrients and Klebsiella possibly outcompete other oral bacteria. The oral and nasal cavities may serve as reservoirs for multiple opportunistic pathogens this way.”
Additionally, Klebsiella can derive nutrients from dead bacteria, allowing it to survive for extended periods under starvation conditions. The researchers found that whenever Klebsiella was present in the oral or nasal samples, they persisted for over 120 days after being deprived of nutrition.
Other notable findings from the study include the observation that Klebsiella from the oral cavity, which harbours a diverse microbial community, was less prevalent and abundant than those from the nasal cavity, a less diverse environment. These findings suggest that microbial diversity and specific commensal (non-pathogenic) saliva bacteria may play a crucial role in limiting the overgrowth of Klebsiella species.
The groundbreaking research conducted by AFI scientists offers new insights into the transmission and spread of hospital-acquired infections, paving the way for more effective prevention and treatment strategies.
Four years ago, a report that a common species of fungus might fuel pancreatic cancer offered a promising new view of the deadly disease. But in working to validate the finding, Duke Health researchers have found no such association. In a study published in the journal Nature, the researchers conducted a multi-pronged analysis of data from the earlier study and found no link between the pancreatic microbiome and the development of pancreatic cancer.
“We were intrigued by the original finding, as were many research teams,” said senior author Peter Allen, MD, professor in the Department of Surgery and chief of the Division of Surgical Oncology at Duke University School of Medicine.
“There is a growing body of literature connecting the human microbiome to disease, and this was particularly compelling for pancreatic cancer,” Allen said. “But our findings did not support an association between fungi and the development of pancreatic cancer in humans.”
Allen and colleagues worked to recreate the 2019 findings published in Nature by a different research team. The original study raised hopes that there might be a possible method of preventing pancreatic cancer with the use of antifungals or some other approach to protect from infection.
Focusing on the research team’s original raw sequencing data, the Duke researchers were unable to reproduce the findings. Additional studies, using pancreatic cancer tissue in Duke repositories, also failed to produce the original results.
“We believe our findings highlight the challenges of using low biomass samples for microbiome sequencing studies,” Allen said. “The inclusion of appropriate negative controls and efforts to identify and remove sequencing contaminants is critical to the interpretation of microbiome data.”
A woman with Systemic Lupus Erythematosus. Source: Wikimedia CC0
Recurrent bouts of systemic lupus erythematosus, marked by the body’s immune system attack of its own tissues, closely tracked with upticks in growth in the gut of a certain species of bacteria. New research from NYU Grossman School of Medicine shows that bacterial blooms of the gut bacterium Ruminococcus blautia gnavus occurred at the same time as disease flare-ups in five of 16 women with lupus of diverse racial backgrounds studied over a four-year period.
Systemic lupus erythematosus involves damaging inflammation, especially in the kidneys, but also in joints, skin, and blood vessels. Four of these study patients with R. gnavus blooms had severe cases of the most common and kidney-specific form of the disease, lupus nephritis, while one had a severe example of lupus involving inflammation in multiple joints.
Published in the Annals of Rheumatic Diseases, the team’s analysis of these lupus patients’ gut bacterial blooms identified 34 genes that already had established links to the bacterium’s growth in people with inflammation. While the specific causes of lupus remain unknown, many experts suspect that bacterial imbalances trigger inherited genetic factors responsible for the disease.
This study also investigated how tightly these patients’ immune system antibodies bonded to structures in the bacterial wall, much like they would an invading virus. These antibodies showed a strong affinity to specific bacterial lipoglycan molecules that are known triggers of inflammation. These lipoglycans were found to be common in R. gnavus strains in lupus patients but not in healthy people. Antibodies are a major cause of the body damage in this disease, and this diagnostic antibody response, the researchers say, highlights the important role played by R. gnavus in the autoimmune disease.
“Our findings provide the strongest evidence to date that silent growths of Ruminococcus blautia gnavus are tied to active serious renal disease in lupus patients,” said study lead investigator Doua Azzouz, PhD.
“Interestingly, our study also established this common bacterial link among a racially diverse group of females with varying forms of lupus,” said Azzouz, a postdoctoral researcher. Lupus is more common in women than in men, and the disease affects more Blacks, Hispanics, and Asians than Whites.
“Our goal is to use our growing understanding of the biological pathways that underpin the disease to develop new treatments that prevent or treat flares for all forms of lupus,” said study senior investigator and immunologist Gregg Silverman, MD.
“Such future treatments for lupus, especially lupus nephritis, could potentially decrease the use of drugs designed to dampen the immune system and instead promote the use of less-toxic antibacterial agents, probiotics or dietary regimens that prevent imbalances such as Ruminococcal blooms in the local gut bacterial population, or microbiome,” said Silverman.
Previous research by Silverman’s team showed that R. gnavus blooms weaken the gut wall barrier, prompting bacterial leakages that in turn trigger inflammatory and overactive immune responses.
The team plans to extend the research to other medical centre and also plans further experiments in mouse models of lupus to see how R. gnavus colonisation triggers lupus. Using mouse models, they also want see whether if R. gnavus blooms speed up or otherwise affect the severity of flares and inflammation.
The researchers say they also want to conduct experiments on various lipoglycan molecules from different R. gnavus strains to see if any particular part of the molecular structure is key to triggering inflammation or if other lipoglycans also prompt an immune response tied to lupus or other diseases of the gut, including Crohn’s.
For the study, researchers used stool and blood samples from lupus patients being treated at NYU Langone. All study participants were being closely monitored for disease flare-ups. Test results were compared with those of 22 female volunteers of similar age and racial background who did not have lupus and were otherwise healthy.
As an autoimmune disease, systemic lupus erythematosus can lead to widespread inflammation and long-term tissue damage in affected organs. According to researchers, about half of patients develop lupus nephritis, of whom one-quarter are likely to experience end-stage renal disease that may require regular blood dialysis and even kidney transplantation.
In spite of burgeoning studies, the biological roots of autism remain elusive. Microbial approaches however have shown some promise, and now a study published in Nature Neuroscience has uncovered a microbial signature associated with autism, which clearly overlaps with metabolic pathways.
The study re-analysed of dozens of previously published datasets and found that they align with a recent, long-term study of autistic individuals that used a microbiome-focused intervention. These findings also underscore the importance of longitudinal studies in elucidating the interplay between the microbiome and complex conditions such as autism.
“We were able to harmonise seemingly disparate data from different studies and find a common language with which to unite them. With this, we were able to identify a microbial signature that distinguishes autistic from neurotypical individuals across many studies,” says Jamie Morton, one of the study’s corresponding authors. “But the bigger point is that going forward, we need robust long-term studies that look at as many datasets as possible and understand how they change when there is a [therapeutic] intervention.”
With 43 authors, this study brought together leaders in computational biology, engineering, medicine, autism and the microbiome who hailed from institutions in North America, South America, Europe and Asia. “The sheer number of fields and areas of expertise in this large-scale collaboration is noteworthy and necessary to get a new and consistent picture of autism,” says Rob Knight, the director of the Center for Microbiome Innovation at the University of California San Diego and a study co-author.
Autism is inherently complex, and studies that attempt to pinpoint specific gut microbes involved in the condition have been confounded by this complexity. First, autism presents in heterogeneous ways – autistic individuals differ from each other genetically, physiologically and behaviourally. Second, the microbiome presents unique difficulties. Microbiome studies typically report simply the relative proportions of specific microbes, requiring sophisticated statistics to understand which microbial population changes are relevant to a condition of interest.
This makes it challenging to find the signal amongst the noise. Making matters more complicated, most studies to date have been one-time snapshots of the microbial populations present in autistic individuals. “A single time point is only so powerful; it could be very different tomorrow or next week,” says study co-author Brittany Needham, assistant professor of anatomy, cell biology and physiology at the Indiana University School of Medicine.
“We wanted to address the constantly evolving question of how the microbiome is associated with autism, and thought, ‘let’s go back to existing datasets and see how much information we may be able to get out of them,'” says co-corresponding author Gaspar Taroncher-Oldenburg, director of Therapeutics Alliances at New York University, who initiated the work with Morton while he was a consultant-in-residence for SFARI.
In the new study, the research team developed an algorithm to re-analyse 25 previously published datasets containing microbiome and other “omic” information, such as gene expression, immune system response and diet, from both autistic and neurotypical cohorts. Within each dataset, the algorithm found the best matched pairs of autistic and neurotypical individuals in terms of age and sex, two factors that can typically confound autism studies.
Novel computational methodologies
“Rather than comparing average cohort results within studies, we treated each pair as a single data point, and thus were able to simultaneously analyse over 600 ASD-control pairs corresponding to a de facto cohort of over 1200 children,” says Taroncher-Oldenburg. “From a technical standpoint, this required the development of novel computational methodologies altogether,” he adds. Their new computational approach enabled them to reliably identify microbes that have differing abundances between ASD and neurotypical individuals.
The analysis identified autism-specific metabolic pathways associated with particular human gut microbes. Importantly, these pathways were also seen elsewhere in autistic individuals, from their brain-associated gene expression profiles to their diets. “We hadn’t seen this kind of clear overlap between gut microbial and human metabolic pathways in autism before,” says Morton.
Even more striking was an overlap between microbes associated with autism, and those identified in a recent long-term faecal microbiota transplant study led by James Adams and Rosa Krajmalnik-Brown at Arizona State University. “Another set of eyes looked at this, from a different lens, and they validated our findings,” says Krajmalnik-Brown, who was not involved in this study.
“What’s significant about this work is not only the identification of major signatures, but also the computational analysis that identified the need for future studies to include longitudinal, carefully designed measurements and controls to enable robust interpretation,” says Kelsey Martin, executive vice president of SFARI and the Simons Foundation Neuroscience Collaborations, who was not involved in the study.
“Going forward, we need more long-term studies that involve interventions, so we can get at cause-and-effect,” says Morton. Taroncher-Oldenburg, who cites the compliance issues often faced by traditional long-term studies, suggests that study designs could more effectively take into account the realities of long-term microbiome sampling of autistic individuals. “Practical, clinical restrictions must inform the statistics, and that will inform the study design,” he says. Further, he points out that long-term studies can reveal insights about both the group and the individual, as well as how that individual responds to specific interventions over time.
Importantly, researchers say these findings go beyond autism. The approach set forth here could also be employed across other areas of biomedicine that have long proved challenging. “Before this, we had smoke indicating the microbiome was involved in autism, and now we have fire. We can apply this approach to many other areas, from depression to Parkinson’s to cancer, where we think the microbiome plays a role, but where we don’t yet know exactly what the role is,” says Knight.
Genes that make bacteria resistant to antibiotics are much more widespread in our environment than was previously realised. A new study published in Microbiome shows that bacteria in almost all environments carry resistance genes, with a risk of them spreading and aggravating the problem of bacterial infections that are untreatable with antibiotics.
“We have identified new resistance genes in places where they have remained undetected until now. These genes can constitute an overlooked threat to human health,” says Erik Kristiansson, a professor in the Department of Mathematical Sciences.
According to the World Health Organisation (WHO), antibiotic resistance is one of the greatest threats to global health. When bacteria become resistant to antibiotics, it becomes difficult or impossible to treat illnesses such as pneumonia, wound infections, tuberculosis and urinary tract infections. According to the UN Interagency Coordination Group on Antimicrobial Resistance (IACG) 700,000 people die each year from infections caused by antibiotic-resistant bacteria.
Looking for resistance genes in new environments
The genes that make bacteria resistant have long been studied, but the focus has traditionally been on identifying those resistance genes that are already prevalent in pathogenic bacteria. Instead, in the new study from Sweden, researchers have looked at large quantities of DNA sequences from bacteria to analyse new forms of resistance genes in order to understand how common they are. They have traced the genes in thousands of different bacterial samples from different environments, in and on people, in the soil and from sewage treatment plants. The study analysed 630 billion DNA sequences in total.
“The data requires a great deal of processing before information can be obtained. We have used metagenomics, a methodology, that allows vast quantities of data to be analysed,” says Juan Inda Díaz, a doctoral student in the Department of Mathematical Sciences, and the article’s lead author.
The study showed that the new antibiotic resistance genes are present in bacteria in almost all environments. This also includes human microbiomes and, more alarmingly, pathogenic bacteria, which can lead to more infections that are difficult to treat. The researchers found that resistance genes in bacteria that live on and in humans and in the environment were ten times more abundant than those previously known. And of the resistance genes found in bacteria in the human microbiome, 75% were not previously known at all.
The researchers stress the need for more knowledge about the problem of antibiotic resistance.
“Prior to this study, there was no knowledge whatsoever about the incidence of these new resistance genes. Antibiotic resistance is a complex problem, and our study shows that we need to enhance our understanding of the development of resistance in bacteria and of the resistance genes that could constitute a threat in the future,” says Kristiansson.
Preventing bacterial outbreaks in healthcare
The research team is currently working on integrating the new data into the international EMBARK project (Establishing a Monitoring Baseline for Antibiotic Resistance in Key environments). The project is coordinated by Johan Bengtsson-Palme, an assistant professor in the Department of Life Sciences at Chalmers, and aims to take samples from sources such as wastewater, soil and animals to get an idea of the way in which antibiotic resistance is spreading between humans and the environment.
“It is essential for new forms of resistance genes to be taken into account in risk assessments relating to antibiotic resistance. Using the techniques we have developed enables us to monitor these new resistance genes in the environment, in the hope that we can detect them in pathogenic bacteria before they are able to cause outbreaks in a healthcare setting,” says Bengtsson-Palme.
The method used by the researchers is called metagenomics, and is not new, but so far has not been used to analyse new types of antibiotic resistance genes in such large quantities. Metagenomics is a method of studying the metagenome, which is the complete gene set of all different organisms in a given sample or within a given environment. Using the method, it is also possible to study microorganisms that cannot be grown in a lab.
